Lectures BENG 212 Winter 2009

Systems Biology and Bioengineering II:

Network Reconstruction & Functional States
Lecture: Tu/Th 2:00 - 3:30 PM in PFBH 161

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Part 1: Reconstruction of networks (BIGG data bases)

Part 2: Properties of reconstructions

Part 3: Methods to determine functional states of networks

2009 Schedule

Date Topic Part Lecturer Material
1/6

1/8
Other

1/13

1/15
Other

1/20

1/22

Other

1/27
1/29
Other

2/3
2/5
Other

2/10
2/12
Other

2/17
2/19
Other

2/24
2/26
Other

3/3
3/5
Other

3/10
3/12
3/13

Course introduction– reconstruction (CH1, CH2, CH5)

E. coli & mircororganisms (CH6, CH7)
Review of Linear Algebra, MatLab, Nat Protocols

Other networks/Human/mammals (CH8, CH9, CH10)

The S-Matrix (CH11)
HW #1: Reconstruct PPS and TCA, combine with glycolysis

The S matrix / topological properties (CH12)

The S matrix / SVD and fundamental subspaces (CH13)

HW#2: compute properties of S from HW1 and core E. coli

SVD/fundamental subspaces/tilting (CH14)
SVD finish/null space (CH14, CH15)
HW #3: ExPA

Left null/row/column spaces of S & Dual causality (CH16, CH17)
Finding functional states (CH18)
Preliminary project reports due 2/12 by midnight

The E. coli core model and COBRA (Appendix)
Exploring capabilites/equivalent solutions (CH19)
HW #4: COBRA basics, functional states of core E.coli

The growth of a cell (CH20, CH21)
Environmental Parameters (CH22)
HW #5: FBA and shadow prices

Genetic Parameters (CH23)
Regulation (CH24)
HW #6: Environemntal and genetic perturbations

Omics and Metabolic Models (CH)
Model-driven discovery (CH28)
HW #7: Randomized sampling and tilting

Adaptive Evolution (CH31)
Metabolic Engineering (CH29, CH30)
Project Presentations 3:15-6:15pm, Fung Auditorium

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JO/RF
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Finals Week
3/16
3/19

Take-home exams due by 6:00pm
Project writeups due




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Location

Location

417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

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